SARS-CoV-2-Queries

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Towards a solution

There is currently no solution for SARS-CoV-2.

But there are ideas about what solutions might be. A vaccine is one of them, but development of that takes time [1]. But there is also talk about antibodies and repurposing of drugs. All this is very much exploratory at this moment. Clinical trials are important (see the Clinical trials section).

This Chapter shows a number of queries with information in Wikidata about leads that people have proposed that may lead to a solution.

Antibodies

Antibodies are getting an interest. The following query lists articles about the human coronaviruses and also annotated with the term ‘antibody’:

SPARQL sparql/antibodies.rq (run, edit)

SELECT ?virus ?virusLabel ?work ?workLabel WITH {
  SELECT ?virus ?work WHERE {
    VALUES ?virus {
      wd:Q82069695 # SARS-CoV-2
      wd:Q16983360 # HKU1
      wd:Q16991954 # OC43
      wd:Q8351095  # NL63 
      wd:Q16983356 # 229E 
      wd:Q4902157  # MERS-CoV
      wd:Q278567   # SARS-CoV
    }
    ?work wdt:P921 ?virus ;
          wdt:P921 wd:Q79460 .
  }
} AS %ARTICLES WHERE {
  INCLUDE %ARTICLES
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
}
ORDER BY ?virusLabel ?virus ?workLabel ?work

The list is getting long, so let’s first show the number of articles about antibodies for each virus:

virus count
SARSr-CoV (edit) 48
Middle East respiratory syndrome coronavirus (edit) 16
SARS-CoV-2 (edit) 13
Human coronavirus 229E (edit) 2
Human coronavirus OC43 (edit) 1

It must be stressed that antibodies are specific for every protein and every coronavirus has different proteins, and this list is just to shortlist relevant literature for reading, not to draw conclusions from:

virus work
Human coronavirus 229E (edit) Antibody to virus components in volunteers experimentally infected with human coronavirus 229E group viruses. (edit)
Human coronavirus 229E (edit) Detection of human coronavirus 229E-specific antibodies using recombinant fusion proteins. (edit)
Human coronavirus OC43 (edit) Development of a recombinant truncated nucleocapsid protein based immunoassay for detection of antibodies against human coronavirus OC43 (edit)
Middle East respiratory syndrome coronavirus (edit) A conformation-dependent neutralizing monoclonal antibody specifically targeting receptor-binding domain in Middle East respiratory syndrome coronavirus spike protein. (edit)
Middle East respiratory syndrome coronavirus (edit) A humanized neutralizing antibody against MERS-CoV targeting the receptor-binding domain of the spike protein. (edit)
Middle East respiratory syndrome coronavirus (edit) A safe and convenient pseudovirus-based inhibition assay to detect neutralizing antibodies and screen for viral entry inhibitors against the novel human coronavirus MERS-CoV (edit)
Middle East respiratory syndrome coronavirus (edit) A truncated receptor-binding domain of MERS-CoV spike protein potently inhibits MERS-CoV infection and induces strong neutralizing antibody responses: implication for developing therapeutics and vaccines (edit)
Middle East respiratory syndrome coronavirus (edit) Exceptionally potent neutralization of Middle East respiratory syndrome coronavirus by human monoclonal antibodies. (edit)
Middle East respiratory syndrome coronavirus (edit) Investigation of anti-middle East respiratory syndrome antibodies in blood donors and slaughterhouse workers in Jeddah and Makkah, Saudi Arabia, fall 2012. (edit)
Middle East respiratory syndrome coronavirus (edit) Middle East respiratory syndrome coronavirus (MERS-CoV) RNA and neutralising antibodies in milk collected according to local customs from dromedary camels, Qatar, April 2014. (edit)
Middle East respiratory syndrome coronavirus (edit) Middle East respiratory syndrome coronavirus antibody reactors among camels in Dubai, United Arab Emirates, in 2005. (edit)
Middle East respiratory syndrome coronavirus (edit) Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study. (edit)
Middle East respiratory syndrome coronavirus (edit) Middle East respiratory syndrome coronavirus spike protein delivered by modified vaccinia virus Ankara efficiently induces virus-neutralizing antibodies. (edit)
This table is truncated. See the full table at sparql/antibodies.rq

Vaccines

In time, we may have a vaccine that could provide us with a level of immunity to protect us against SARS-CoV-2. Several vaccines-candidates are being studied right now [2]. We can list the vaccines given in Wikidata with this query:

SPARQL sparql/vaccines.rq (run, edit)

SELECT DISTINCT ?vaccine ?vaccineLabel ?type ?typeLabel WHERE {
  VALUES ?for { wd:Q84263196 }
  ?vaccine wdt:P31 / wdt:P279? wd:Q134808 ;
           wdt:P1924 ?for .
  ?vaccine wdt:P31 ?type .
  FILTER ( ?type != wd:Q28051899 ) FILTER ( ?type != wd:Q98734151 )
  FILTER ( ?type != wd:Q87719492 ) FILTER ( ?type != wd:Q30612 )
  FILTER ( ?type != wd:Q134808 )
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
} ORDER BY ASC(?vaccine) ASC(?type)

It currently list not many:

vaccine type
Sanofi/GSK SARS-CoV-2 subunit vaccine (edit) protein subunit vaccine (edit)
UB-612 (edit) protein subunit vaccine (edit)
RBD SARS-CoV-2 HBsAg VLP (edit) virus-like particle vaccine (edit)
bacTRL-Spike (edit) DNA vaccine (edit)
hAd5-S-Fusion+N-ETSD (edit) adenovirus-based vaccine (edit)
VXA-CoV2-1 (edit) adenovirus-based vaccine (edit)
MVC-COV1901 (edit) protein subunit vaccine (edit)
FINLAY-FR-2 (edit) conjugate vaccine (edit)
mRNA-1273 (edit) RNA vaccine (edit)
AZD1222 (edit) adenovirus-based vaccine (edit)
Ad5-nCoV (edit) adenovirus-based vaccine (edit)
INO-4800 (edit) DNA vaccine (edit)
ZyCoV-D (edit) DNA vaccine (edit)
This table is truncated. See the full table at sparql/vaccines.rq

Clinical trials

While far from complete, clinical trials registered in clinicaltrials.gov are finding their way into Wikidata. The following query lists a number of clinical trials with COVID-19 as main topic:

SPARQL sparql/clinicalTrials.rq (run, edit)

SELECT ?trial ?trialLabel ?intervention ?interventionLabel ?phase ?phaseLabel ?identifier WHERE {
  VALUES ?topic {
    wd:Q84263196 wd:Q82069695
  }
  ?trial wdt:P31 wd:Q30612 ;
         wdt:P921 ?topic ;
         wdt:P6099 ?phase ;
         wdt:P3098 ?identifier .
  OPTIONAL {
    ?trial wdt:P4844 ?intervention .
  }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
} ORDER BY DESC(?identifier) ASC(?intervention)

This lists has become very long, and click one of the above links to list them all, and only 15 are given here:

trial intervention phase identifier
A Randomised, Controlled, Phase 1 Study to Evaluate the Safety and Immunogenicity of a Candidate Adjuvanted Recombinant Protein SARS-COV-2 Vaccine in Healthy Adult Subjects (edit) COVAX-19 (edit) phase I clinical trial (edit) NCT04453852
An Adaptive Study of Favipiravir Compared to Standard of Care in Hospitalized Patients With COVID-19 (edit) hydroxychloroquine (edit) phase II clinical trial (edit) NCT04434248
An Adaptive Study of Favipiravir Compared to Standard of Care in Hospitalized Patients With COVID-19 (edit) hydroxychloroquine (edit) phase III clinical trial (edit) NCT04434248
An Adaptive Study of Favipiravir Compared to Standard of Care in Hospitalized Patients With COVID-19 (edit) chloroquine (edit) phase II clinical trial (edit) NCT04434248
An Adaptive Study of Favipiravir Compared to Standard of Care in Hospitalized Patients With COVID-19 (edit) chloroquine (edit) phase III clinical trial (edit) NCT04434248
An Adaptive Study of Favipiravir Compared to Standard of Care in Hospitalized Patients With COVID-19 (edit) lopinavir (edit) phase II clinical trial (edit) NCT04434248
An Adaptive Study of Favipiravir Compared to Standard of Care in Hospitalized Patients With COVID-19 (edit) lopinavir (edit) phase III clinical trial (edit) NCT04434248
An Adaptive Study of Favipiravir Compared to Standard of Care in Hospitalized Patients With COVID-19 (edit) ritonavir (edit) phase II clinical trial (edit) NCT04434248
An Adaptive Study of Favipiravir Compared to Standard of Care in Hospitalized Patients With COVID-19 (edit) ritonavir (edit) phase III clinical trial (edit) NCT04434248
Dose-Confirmation Study to Evaluate the Safety, Reactogenicity, and Immunogenicity of mRNA-1273 COVID-19 Vaccine in Adults Aged 18 Years and Older (edit) mRNA-1273 (edit) phase II clinical trial (edit) NCT04405076
Study of the Efficacy and Safety of a Single Administration of Olokizumab and RPH-104 With Standard Therapy in Patients With Severe Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection (COVID-19) (edit) phase II clinical trial (edit) NCT04380519
Study of the Efficacy and Safety of a Single Administration of Olokizumab and RPH-104 With Standard Therapy in Patients With Severe Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection (COVID-19) (edit) phase III clinical trial (edit) NCT04380519
Study to Describe the Safety, Tolerability, Immunogenicity, and Potential Efficacy of RNA Vaccine Candidates Against COVID-19 in Healthy Adults (edit) tozinameran (edit) phase I clinical trial (edit) NCT04368728
This table is truncated. See the full table at sparql/clinicalTrials.rq

Drug repurposing

The Section 8.3 already listed an overview of clinical trials. It gives an idea of what symptoms people are worried about. It also gives insight in what drugs are studied for repurposing. Some of these have received a lot of attention, others less so. They look like this:

The following query lists the number of clinical trials by intervention:

SPARQL sparql/clinicalTrialsByIntervention.rq (run, edit)

SELECT ?intervention ?interventionLabel (COUNT(?trial) AS ?trials) WHERE {
  VALUES ?topic {
    wd:Q84263196 wd:Q82069695
  }
  ?trial wdt:P31 wd:Q30612 ;
         wdt:P921  ?topic ;
         wdt:P4844 ?intervention .
  SERVICE wikibase:label { bd:serviceParam wikibase:language "en,en". }
} GROUP BY ?intervention ?interventionLabel
  ORDER BY DESC(?trials) ASC(?intervention)

This gives:

intervention trials
hydroxychloroquine (edit) 43
chloroquine (edit) 15
lopinavir (edit) 15
ritonavir (edit) 15
Chloroquine diphosphate bearing dextran nanoparticles augmented drug delivery and overwhelmed drug resistance in Plasmodium falciparum parasites (edit) 12
COVID-19 (edit) 11
tocilizumab (edit) 6
interferon (edit) 4
nitric oxide (radical) (edit) 4
antiviral agent (edit) 4
losartan (edit) 4
paracetamol (edit) 4
prednisolone (edit) 3
This table is truncated. See the full table at sparql/clinicalTrialsByIntervention.rq

Importantly, this list only gives an idea of what intervention have received more attention than others. And it is essential to realize that attention is not a measure of success.

References

  1. Lu S, Lu S. Timely development of vaccines against SARS-CoV-2. Emerging microbes & infections. 2020 Mar 8;9(1):542–4. doi:10.1080/22221751.2020.1737580 (Scholia)
  2. Le TT, Andreadakis Z, Kumar A, Román RG, Tollefsen S, Saville M, et al. The COVID-19 vaccine development landscape. Nat Rev Drug Discov. 2020 Apr 9; doi:10.1038/D41573-020-00073-5 (Scholia)